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Originally published as Genetics Published Articles Ahead of Print on April 2, 2006.
Genetics, Vol. 173, 1075-1087, June 2006, Copyright © 2006
doi:10.1534/genetics.106.055871
Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map
Hans van Os*,
Sandra Andrzejewski
,
Erin Bakker
,
Imanol Barrena
,
Glenn J. Bryan**,
Bernard Caromel,
Bilal Ghareeb,
Edwige Isidore**,
Walter de Jong**,1,
Paul van Koert,2,
Véronique Lefebvre,
Dan Milbourne**,3,
Enrique Ritter,
Jeroen N. A. M. Rouppe van der Voort,2,
Françoise Rousselle-Bourgeois,
Joke van Vliet,
Robbie Waugh**,
Richard G. F. Visser*,
Jaap Bakker and
Herman J. van Eck*,4
* Laboratory of Plant Breeding, Wageningen University, 6700 AJ Wageningen, The Netherlands, Laboratory of Nematology, Wageningen University, 6709 PD Wageningen, The Netherlands, ** Genome Dynamics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Station de Génétique et Amélioration des Fruits et Légumes, Institut National de la Recherche Agronomique, 84143 Monfavet Cedex, France and NEIKER, E-01080 Vitoria, Spain
4 Corresponding author: Laboratory of Plant Breeding, Department of Plant Sciences, Graduate School Experimental Plant Sciences, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.
E-mail: herman.vaneck{at}wur.nl
An ultradense genetic linkage map with >10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in "skeleton bin maps," which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in "bins." A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).
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